SLC44A3
protein-codingsolute carrier family 44 member 3, the group of Solute carrier family 44
Gene summary
Predicted to enable transmembrane transporter activity. Predicted to be involved in transmembrane transport. Predicted to be located in plasma membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~74.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SLC44A3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001114106.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 4 | 4 | ||||
| missense | 79 | 7 | 86 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 5 | 5 | ||||
| Total | 0 | 0 | 89 | 7 | 0 | 96 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001107578.1 | 15 | MANE Select | |
| Ensembl | ENSP00000271227.6 | 15 | MANE Select | |
| RefSeq | NP_001245269.1 | 15 | Standard | |
| RefSeq | NP_001245270.1 | 15 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Choline metabolism in cancer - Homo sapiens (human)
- Metabolism of lipids
- Amine compound SLC transporters
- Metabolism
- Transport of bile salts and organic acids, metal ions and amine compounds
Biological Process
- phosphatidylcholine biosynthetic process
- choline transport
- transmembrane transport
Molecular Function
- protein binding
- choline transmembrane transporter activity
Cellular Component
- plasma membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000271227
- Coding exons
- 15
- Length
- 74905
- Individuals with no LoFs
- 125551
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 197
- Defined
- 125748
- p
- 0.000784
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.994 | 291 | 343 | 0.849 | 0.0000172 | 4272 |
| Missense (PolyPhen) | 86 | 105.11 | 0.81817 | 1408 | ||
| Synonymous | 0.965 | 125 | 139 | 0.896 | 0.00000784 | 1249 |
| Loss of Function | -0.669 | 38 | 33.8 | 1.12 | 0.00000177 | 400 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0025 | 0.0025 | notable |
| Latino/Admixed American | 0.00041 | 0.00032 | rare |
| Ashkenazi Jewish | 0.00060 | 0.00060 | rare |
| East Asian | 0.0034 | 0.0033 | notable |
| Finnish | 0.000047 | 0.000046 | rare |
| European (Non-Finnish) | 0.00057 | 0.00057 | rare |
| South Asian | 0.00044 | 0.00039 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.0935
Intolerance Scores
- LoFtool
- 0.996
- RVIS EVS
- -0.02
- RVIS percentile EVS
- 52.25
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.701
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |